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- PDB-6sbj: X-ray structure of mus musculus Fumarylacetoacetate hydrolase dom... -

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Basic information

Entry
Database: PDB / ID: 6sbj
TitleX-ray structure of mus musculus Fumarylacetoacetate hydrolase domain containing protein 1 (FAHD1) apo-form uuncomplexed
ComponentsAcylpyruvase FAHD1, mitochondrial
KeywordsHYDROLASE
Function / homology
Function and homology information


acylpyruvate hydrolase / fumarylpyruvate hydrolase activity / acylpyruvate hydrolase activity / Citric acid cycle (TCA cycle) / acetylpyruvate hydrolase activity / oxaloacetate decarboxylase / oxaloacetate decarboxylase activity / mitochondrial inner membrane / mitochondrion / nucleoplasm ...acylpyruvate hydrolase / fumarylpyruvate hydrolase activity / acylpyruvate hydrolase activity / Citric acid cycle (TCA cycle) / acetylpyruvate hydrolase activity / oxaloacetate decarboxylase / oxaloacetate decarboxylase activity / mitochondrial inner membrane / mitochondrion / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase family / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Acylpyruvase FAHD1, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsRupp, B. / Naschberger, A. / Weiss, A.K.H.
Funding support Austria, 2items
OrganizationGrant numberCountry
European Commission512020 Austria
Austrian Science FundP28395-B26 Austria
CitationJournal: Biosci.Rep. / Year: 2020
Title: Structural and functional comparison of fumarylacetoacetate domain containing protein 1 in human and mouse.
Authors: Weiss, A.K.H. / Naschberger, A. / Cappuccio, E. / Metzger, C. / Mottes, L. / Holzknecht, M. / von Velsen, J. / Bowler, M.W. / Rupp, B. / Jansen-Durr, P.
History
DepositionJul 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acylpyruvase FAHD1, mitochondrial
B: Acylpyruvase FAHD1, mitochondrial
C: Acylpyruvase FAHD1, mitochondrial
D: Acylpyruvase FAHD1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,01116
Polymers117,6524
Non-polymers35912
Water2,072115
1
A: Acylpyruvase FAHD1, mitochondrial
B: Acylpyruvase FAHD1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0058
Polymers58,8262
Non-polymers1796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-76 kcal/mol
Surface area16660 Å2
MethodPISA
2
C: Acylpyruvase FAHD1, mitochondrial
D: Acylpyruvase FAHD1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0058
Polymers58,8262
Non-polymers1796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-74 kcal/mol
Surface area15800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.401, 69.959, 107.557
Angle α, β, γ (deg.)90.000, 92.250, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRARGARGAA10 - 22448 - 262
21THRTHRARGARGBB10 - 22448 - 262
12PROPROSERSERAA12 - 22550 - 263
22PROPROSERSERCC12 - 22550 - 263
13LYSLYSSERSERAA11 - 22549 - 263
23LYSLYSSERSERDD11 - 22549 - 263
14PROPROARGARGBB12 - 22450 - 262
24PROPROARGARGCC12 - 22450 - 262
15LYSLYSARGARGBB11 - 22449 - 262
25LYSLYSARGARGDD11 - 22449 - 262
16PROPROARGARGCC12 - 22450 - 262
26PROPROARGARGDD12 - 22450 - 262

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Acylpyruvase FAHD1, mitochondrial / Fumarylacetoacetate hydrolase domain-containing protein 1 / Oxaloacetate decarboxylase / OAA decarboxylase


Mass: 29412.994 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fahd1, MNCb-4134 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8R0F8, acylpyruvate hydrolase, oxaloacetate decarboxylase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.68 Å3/Da / Density % sol: 27 % / Description: thin needles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% (w/v) PEG 3350, 0.2 M MgCl2 and 0.1 M Bis/Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 20, 2018
RadiationMonochromator: Diamond C110 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.217→42.65 Å / Num. obs: 26144 / % possible obs: 89.2 % / Redundancy: 3.44 % / Biso Wilson estimate: 22.6 Å2 / CC1/2: 0.963 / Rmerge(I) obs: 0.251 / Rpim(I) all: 0.159 / Rrim(I) all: 0.298 / Net I/σ(I): 4.6
Reflection shellResolution: 2.217→2.466 Å / Redundancy: 3.38 % / Rmerge(I) obs: 0.958 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1316 / CC1/2: 0.553 / Rpim(I) all: 0.609 / Rrim(I) all: 1.138 / % possible all: 45.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FOH

6foh


Resolution: 2.22→42.65 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.881 / SU ML: 0.398 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.521 / SU Rfree Cruickshank DPI: 0.341
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 1219 4.7 %RANDOM
Rwork0.1933 ---
obs0.1962 24929 67.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 134.31 Å2 / Biso mean: 27.656 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20.56 Å2
2---0.02 Å20 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 2.22→42.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6449 0 12 115 6576
Biso mean--22.85 13.23 -
Num. residues----832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136651
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176449
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.6329007
X-RAY DIFFRACTIONr_angle_other_deg1.2221.57615010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1295833
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.69621.796284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.104151189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6391538
X-RAY DIFFRACTIONr_chiral_restr0.0660.2860
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027256
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021318
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A63580.1
12B63580.1
21A62470.1
22C62470.1
31A62610.1
32D62610.1
41B62730.08
42C62730.08
51B63020.08
52D63020.08
61C62670.08
62D62670.08
LS refinement shellResolution: 2.22→2.273 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.345 3 -
Rwork0.265 142 -
obs--5.08 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.32980.0398-0.10660.1442-0.12480.1577-0.02080.03720.00050.00770.00930.0218-0.01410.01880.01150.07720.0023-0.02580.0578-0.00620.112123.32943.047842.3992
20.26780.01180.0830.1553-0.10690.1618-0.0082-0.02930.01440.00370.00790.0205-0.00140.0020.00020.0724-0.0046-0.01430.0601-0.00810.12066.2583-3.127962.1109
30.6217-0.2879-0.09450.218-0.31841.9043-0.13130.04790.0880.00650.0719-0.05920.1396-0.34150.05940.1021-0.0811-0.0080.1546-0.01870.01719.6358-26.0628-8.7037
40.30010.03730.23570.3046-0.53791.2997-0.0704-0.0479-0.06010.0338-0.0009-0.0922-0.0983-0.10640.07140.07510.0001-0.04580.07710.03120.078816.3816-25.441717.3087
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 225
2X-RAY DIFFRACTION2B5 - 225
3X-RAY DIFFRACTION3C12 - 225
4X-RAY DIFFRACTION4D11 - 225

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